AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user.

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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Machine learning

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Swarm intelligence is a relatively new approach to problem solving that takes inspiration from the social behaviors of insects and of other animals In particular, ants have inspired a number of methods and techniques among which the most studied and the most successful is the general purpose optimization technique known as ant colony optimization Ant colony optimization (ACO) takes inspiration from the foraging behavior of some ant species These ants deposit pheromone on the ground in order to mark some favorable path that should be followed by other members of the colony Ant colony optimization exploits a similar mechanism for solving optimization problems From the early nineties, when the first ant colony optimization algorithm was proposed, ACO attracted the attention of increasing numbers of researchers and many successful applications are now available Moreover, a substantial corpus of theoretical results is becoming available that provides useful guidelines to researchers and practitioners in further applications of ACO The goal of this article is to introduce ant colony optimization and to survey its most notable applications

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Ant Colony Optimization

In this paper, we intend to formulate a new meta-heuristic algorithm, called Cuckoo Search (CS), for solving optimization problems. This algorithm is based on the obligate brood parasitic behaviour of some cuckoo species in combination with the Levy flight behaviour of some birds and fruit flies. We validate the proposed algorithm against test functions and then compare its performance with those of genetic algorithms and particle swarm optimization. Finally, we discuss the implication of the results and suggestion for further research.

Cuckoo Search via Lévy flights

The field of metaheuristics for the application to combinatorial optimization problems is a rapidly growing field of research. This is due to the importance of combinatorial optimization problems for the scientific as well as the industrial world. We give a survey of the nowadays most important metaheuristics from a conceptual point of view. We outline the different components and concepts that are used in the different metaheuristics in order to analyze their similarities and differences. Two very important concepts in metaheuristics are intensification and diversification. These are the two forces that largely determine the behavior of a metaheuristic. They are in some way contrary but also complementary to each other. We introduce a framework, that we call the I&D frame, in order to put different intensification and diversification components into relation with each other. Outlining the advantages and disadvantages of different metaheuristic approaches we conclude by pointing out the importance of hybridization of metaheuristics as well as the integration of metaheuristics and other methods for optimization.

/pdf/metaheuristics-in-combinatorial-optimization-overview-and-menr0q3bxw.pdf

Metaheuristics in combinatorial optimization: Overview and conceptual comparison

http://mahdimaherani.persiangig.com/document/Ant%20colony%20optimization%20theory%20A%20survey.pdf

Ant colony optimization theory: a survey

http://personal.cimat.mx:8181/~jortega/MaterialDidactico/modestoI10/Proyectos/Blum%20%282005%29AntCol.pdf

Ant colony optimization: Introduction and recent trends

Research in metaheuristics for combinatorial optimization problems has lately experienced a noteworthy shift towards the hybridization of metaheuristics with other techniques for optimization. At the same time, the focus of research has changed from being rather algorithm-oriented to being more problem-oriented. Nowadays the focus is on solving the problem at hand in the best way possible, rather than promoting a certain metaheuristic. This has led to an enormously fruitful cross-fertilization of different areas of optimization. This cross-fertilization is documented by a multitude of powerful hybrid algorithms that were obtained by combining components from several different optimization techniques. Hereby, hybridization is not restricted to the combination of different metaheuristics but includes, for example, the combination of exact algorithms and metaheuristics. In this work we provide a survey of some of the most important lines of hybridization. The literature review is accompanied by the presentation of illustrative examples.

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Hybrid metaheuristics in combinatorial optimization: A survey

Keywords: Swarm Intelligence ; Collective Robotics ; SWARM_BOTS ; Evolutionary Robotics Note: Proceedings of the ANTS 2004, 4th International Workshop Sponsor: swarm-bots, OFES 01-0012-1 Reference LIS-BOOK-2004-002 URL: http://iridia.ulb.ac.be/~ants/ants2004/ Record created on 2006-01-12, modified on 2017-05-10

Christian Blum

Papers

Metaheuristics in combinatorial optimization: Overview and conceptual comparison

Ant colony optimization theory: a survey

Ant colony optimization: Introduction and recent trends

Hybrid metaheuristics in combinatorial optimization: A survey

Ant Colony Optimization and Swarm Intelligence